I've tried doing the below from the FAQ (from just after the word NOTE), but to no avail, to prevent thumbnails from showing up inside the gallery. How do I "not attach a photo" to a post in which I'm using that photo?
"C. Right after that starting on a new line, insert all other images you want to show in your gallery. You can even use the WordPress internal gallery feature with the shortcode [gallery link="file"]. NOTE: if the gallery thumbnail is attached to the post, it will be show a second time when flipping through the gallery in FancyBox. If you do not want that, use an image that is not attached to the post as gallery thumbail."